import numpy as np
from scipy.io import mmread
import pandas as pd
import anndata as ad
def read_ATAC_10x(matrix, cell_names='', var_names='', path_file=''):
"""
Load sparse matrix (including matrices corresponding to 10x data) as AnnData objects.
read the mtx file, tsv file coresponding to cell_names and the bed file containing the variable names
Parameters
----------
matrix: sparse count matrix
cell_names: optional, tsv file containing cell names
var_names: optional, bed file containing the feature names
Return
------
AnnData object
"""
mat = mmread(''.join([path_file, matrix]))
mat = mat.toarray()
mat = np.matrix(mat.transpose())
with open(path_file+cell_names) as f:
barcodes = f.readlines()
barcodes = [x[:-1] for x in barcodes]
with open(path_file+var_names) as f:
var_names = f.readlines()
var_names = ["_".join(x[:-1].split('\t')) for x in var_names]
adata = ad.AnnData(mat, obs=pd.DataFrame(index=barcodes), var=pd.DataFrame(index=var_names))
adata.uns['omic'] = 'ATAC'
return(adata)
